chris1221 / ancient_african_admixture

Cole et al 2021 analysis pipeline and result files.

Ancient Admixture into Africa

This repository contains all of the source code required to reproduce our paper on ancient directional migration using an extention of smcsmc.

• pipelines/ contains two different pipelines which implement all of the analyses in the paper. The first uses smcsmc and msmc2 to analyse real data from the SGDP and HGDP. The second uses scrm to simulate demographic scenarios and does inference with smcsmc and msmc. For instructions on reproducing these results, see directions in these directories. As a forewarning, these analyses are highly computationally intensive and may take several weeks or months of compute to run completely.
• data/ contains all of the relevant results from the pipelines/ directory used in the paper, and in the plots.
• r/ contains scripts for reproducing all of the plots from the paper. Note that r/MASTER.r, if run by itself, contains all of the code necessary to create all the plots using the data in the data/ directory.
• plot/ has the output of the r/ directory, which are the plots used in the paper.
• tex/ has the LaTeX source for the actual manuscript of the paper.
• analyses contains configuration files for the different analyses performed using the pipelines. Similarly, lib/ has some useful files for the plotting scripts.

Setting up the Environment

To reproduce the analysis completely, please install the required conda environment. This allows us to package a majority of the software dependencies together. There are several methods to install conda, see here for details. Once conda is installed, create the environment for this analysis from our list of dependencies:

conda env create -f envs/aaa.yml

This will create a conda environemnt called aaa. Activate it:

conda activate aaa

There are a couple of dependencies that are not included in conda and must be installed manually.

• msmc2 must be installed from the Github source here.
• admixr must be installed from Github as well.

install.packages("devtools")
devtools::install_github("bodkan/admixr")